1TSU

CRYSTAL STRUCTURE OF DECAMER NCP1 SUBSTRATE PEPTIDE IN COMPLEX WITH WILD-TYPE D25N HIV-1 PROTEASE VARIANT


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MTR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2298SODIUM PHOSPHATE, SODIUM CITRATE, AMMONIUM SULPHATE, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0138.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.058α = 90
b = 57.731β = 90
c = 61.495γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray220IMAGE PLATERIGAKU RAXISOSMIC MIRRORS2002-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.142.2694.10.0921045010450-3-3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1MTR2.142.26-39912991249393.930.207170.205870.23355RANDOM40.067
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-1-0.341.34
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it9.961
r_scbond_it7.225
r_mcangle_it5.128
r_dihedral_angle_1_deg4.286
r_mcbond_it3.623
r_angle_refined_deg1.462
r_xyhbond_nbd_refined0.52
r_symmetry_vdw_refined0.465
r_symmetry_hbond_refined0.31
r_nbd_refined0.248
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it9.961
r_scbond_it7.225
r_mcangle_it5.128
r_dihedral_angle_1_deg4.286
r_mcbond_it3.623
r_angle_refined_deg1.462
r_xyhbond_nbd_refined0.52
r_symmetry_vdw_refined0.465
r_symmetry_hbond_refined0.31
r_nbd_refined0.248
r_chiral_restr0.178
r_gen_planes_refined0.017
r_bond_refined_d0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1526
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing